Replace the timing chain. Check the transmission gears for pitting and replace if there is any. Try to replace the timing chain sprockets too. Of course replace the timing chain guides. I have a couple of them and a bunch of other XR600 parts from a 1985 XR600. You or somebody like you should have me ship all the xr600 parts to you for cheap. Get new rings and have a machinist micrometer measure the cylinder and piston and advise a rebore or hone and new rings. The gasket kit you are ordering will likely NOT include the proper rocker box gasket, so make sure to order that from Honda or someone stocking genuine Honda parts. That is the one important gasket to have, any other one will have your cam bearings improperly torqued and/or leaking rocker box. Also go ahead and spray that gasket with copper coat in an aerosol can and it will never leak. It is the most temperamental seal in the entire engine. Also be sure to install the cam chain tensioner with great care. It is a sensitive device. Go ahead and buy a new spring for it, it is not externally adjustable, so be very nice to it and treat it like a beautiful woman you're about to make love to all night long. Or something like that.
The valves should at least be removed and lapped with a valve lapping compound and washed thoroughly. Remember you can reassemble the transmission without a gasket and test shift it before final assembly. Also check the kickstart idle shaft bushings. I had one of those making wierd noises once, and the shaft it rode on (main or counter transmission shaft) was pitted. I have a ton of XR600R 1985 parts if you want them, just pay shipping plus tip. Look forward to the build.